The Reason
by aznange139
Summary: Ever wonder exactly why Shepard is working for Cerberus? Or how would Kaidan react to finding out the truth behind it? What about her response to his email? Or all of the romance from ME1 to ME2? This is my take on all of it.


**DISCLAIMER:**

I own nothing here. Kaidan, Anderson, and everything else is owned rightfully by BioWare. This is all for fun...Blah Blah Blah. I'm sure you get the idea.  
Though I guess, I indirectly own the idea behind Diana Shepard (Paragon, Spacer, Akuze Background)? No, I'll stick with BioWare owning everything! Better safe than sorry!

* * *

Kaidan didn't know how he felt after that incident with Diana a few minutes ago on the surface of Horizon. He could hear her ship take off in the distance, and part of him regretted not being able to go with her. But he had to remind himself that she has become allies with Cerberus, the one company that has caused so much problems for them in the past when they were hunting down Saren two years ago.

He entered the cramped living space of his quarters on the ship the Alliance assigned to him. The _SSV Washington _was a good ship, but it was nothing like the Normandy. Looking around, Kaidan's eyes fell onto the picture of the woman he loved, the woman he though was dead until a few minutes ago.

Rationally, he knew that she spoke the truth to him. She wouldn't do this if it wasn't right. He knew that there was a chance Diana was right, that he was letting his emotions get the better of him and preventing him from seeing the evidence in his face. He had to explain himself to her. He had to try. He just hoped he wasn't too late.

Deciding it would be best to just contact her and apologize for his actions would be a start. He knew she might not get it, or even respond if she did, but he would feel a little bit better if he at least attempted to tell her how he felt. Sitting down at his private terminal, he began typing a message to his former lover. He wanted to tell her everything, that his heart never truly let her go.

*~*~*~*~ **SCENE CHANGE** ~*~*~*~*

Commander Diana Shepard could not believe her luck. As she was finishing up Legion's personal mission, the Collectors came and took every single person on the Normandy. Joker was the only one lucky enough to escape their clutches and save the ship. She didn't even know about it until she returned to find the ship completely empty with the exception of her pilot. She walked into her private quarters to change out of her battle gear into her normal deck outfit.

As she began to feed the fish before they died again, she heard a beep from her private terminal indicating that she had received a new message. Walking over, she carefully sat down at her desk once she read the subject line of the incoming message.

_**Diana,**_

_**I'm sorry for what I said back on Horizon. I spent two years ****pulling myself back together after you went down with the Normandy. It took me a long time to get over my guilt for surviving and move on. I'd finally let my friends talk me into going out for drinks with a doctor on the Citadel. Nothing serious, but trying to let myself have a life again, you know?**_

_**Then I saw you again and everything pulled hard to port. You were standing in front of me, but you were with Cerberus. I guess I really don't know who either of us is anymore. Do you even remember that night before Ilos? That night meant everything to me...maybe it meant as much to you. But a lot has changed in the last two years and I can't just put that aside. But please be careful.**_

_**I've watched too many people close to me die – on Eden Prime, on Virmire, on Horizon, on the Normandy. I couldn't bear it if I lost you again. If you're still the woman I remember, I know you'll find a way to stop these Collector attacks. But Cerberus is too dangerous to be trusted. Watch yourself. When things have settled down a little...maybe...I don't know. Just take care.**_

_**- Kaidan**_

Diana didn't know whether she wanted to jump for joy or cry her heart out. She understood where Kaidan was coming from, why he felt the way he did about her "return". To her, it was like it was only yesterday that she was telling him to evacuate the crew. To him, it's been a painful two years moving on. She didn't want to make it more painful by telling him the reason she was stuck with Cerberus in the first place. She knew that he had every right to know the truth, especially when it concerned him as well. But, there was no way she could directly tell him the reason while being aboard a Cerberus ship.

As much as she wanted to tell him everything, Diana decided that it would be better if she waited until the last possible second to do so. Carefully, she considered her words as she typed up the message that she was going to send him. She knew the only way to explain things to him in case she didn't make it would be to send him another message right before they entered the Omega 4 Relay.

It was the best way to ensure EDI couldn't let the Illusive Man know about her message to Kaidan, telling him everything he needed to know about this mission and what he'll need to do against the Collectors and Reapers. That was her only choice.

*~*~*~*~ **SCENE CHANGE** ~*~*~*~*

Dealing with the Council was difficult. Once he arrived on the Citadel, Kaidan immediately reported to the Anderson and the rest of the Council to give his report from Horizon. He decided it would be best not to mention the little confrontation that he had with Diana. He wasn't too surprised when he found out that she was reinstated to Spectre status once the Council confirmed she was alive. He WAS surprised that she even went to the Council to tell them what she had discovered and try to get their help on the matter.

"Commander Alenko's report just indicates the Cerberus was conveniently there on Horizon as the colonists were taken away, along with Commander Shepard." Kaidan was really starting to dislike the Turian Councilor. He tried his best to keep the reports from Horizon unbiased and completely neutral so that they couldn't say such things to him.

"This could mean that she is helping Cerberus with their new 'project' on humans," the Salarian Councilor agreed. Kaidan was getting very tempted to punch one of these Council members, and if it wasn't for Anderson standing next to him, he just might have if they were actually there. His omni-tool began to beep, notifying him of an incoming message.

"I have told you that Commander Shepard is the reason that not all of the colonists were kidnapped by the Collectors on Horizon. Commander Alenko's reports support Shepard's initial findings from when she spoke with you several weeks ago," Anderson stated.

"I have nothing else to report on the matter Council. Now, If you would excuse me for a moment." Kaidan walked over to a corner of Anderson's office so that he could read the message that he just received. He was completely surprised when he realized that Diana had responded to his message. He carefully read each line, his entire body becoming more and more rigid the more he read the message. By the time he was finished, Kaidan felt like he could hardly breathe and was the worst person for saying what he did to the woman he loved.

_** Kaidan -**_

_**I understand why you were angry, you don't have to apologize for what happened back there. I have so much to tell you Kaidan, I really do. Please believe me when I say that. **_

_**I know Cerberus can't be trusted, and they're probably tracking this as I write to you. I know they are using me for their own reasons, but I won't make it easy for them. I want to tell you though, there is a reason I'm doing this, working for Cerberus. Hopefully, I can tell you one day, but not now. I will find a way to explain at least my actions to work with them to you someday. Trust me when I say that. **_

_**I won't lie to you Kaidan, this is most likely a suicide mission. I might not make it back. I know it's cruel of me to say I will explain things to you and then tell you I might not survive this. I want you to know that I never stopped thinking about you. I want you to continue with your life if I don't make it back. I doubt Cerberus will want to raise me from the dead a second time. Just know that I'm fighting for the right reasons. I have people I want to protect, people that mean everything to me. I promise it will make sense later. It will. There's just one thing I want you to know, so don't ever doubt this. **_

_**Kaidan Alenko, I love you. **_

_**Regards, Diana**_

Kaidan didn't even realize he was standing there for so long until Anderson began to lead him towards an open seat in the office after ending the meeting with the Council.

"Thanks Councilor," he mumbled.

"I take it you received some news that you're not happy about from Shepard?" Despite having a feeling that Alenko and Shepard had become more personal since she became CO of the Normandy, Anderson never reprimanded the two because of everything they've been through. Shepard commanded the Normandy, and the entire crew was loyal to her. She had that aura about her where people were drawn to her and wanted to make sure she succeeded in everything she did. Even though Anderson could tell the two of them deeply cared for each other, they presented themselves with a level of professionalism that would not allow their feelings to get in the way of their duty.

"You could say that. Not necessarily bad news, but not the best news either." Kaidan sighed.

"Mind telling me what's going on?" Anderson asked.

"Mostly, Shepard and I did not part on very good terms on Horizon. I was upset that she's been around for so long and didn't try to tell me." The Human Councilor let out a sigh of his own before telling Kaidan the reason Shepard wasn't capable of contacting him.

"I'm sorry Alenko, but she did try to contact you. I didn't tell her where you were though." Kaidan's head shot up and he instantly looked at Anderson.

"WHAT?" Kaidan couldn't believe that Diana was actually trying to find him. And he so readily accused her of not caring about him.

"Alenko, you were on a highly-classified mission to determine if Cerberus was behind the missing colonies. I couldn't risk telling Shepard that while she's under their watch. She kept insisting, but I wouldn't budge, no matter how much I know Shepard wouldn't betray us." Kaidan's shoulder's fell since he couldn't really blame Anderson for his reasoning in keeping Shepard in the dark.

"I know Sir. It's just....it's like the time with Saren. She says this is more dangerous than it was before. But now she has a completely new crew, and no one else to back her up on this."

"I won't lie to you, but it just might be that way. Reports indicated that Garrus, Tali, Joker, and Dr. Chakwas are the only people from the original crew aboard the new Normandy. Also, if they go through the Omega 4 Relay, there's a chance they won't make it back. No ship has every returned from there." Anderson and Kaidan both knew what that statement indicated. Once they pass through the relay, Shepard and the rest of the crew might never come back.

Suddenly, Ambassador Udina walked into Anderson's office with some news they needed to hear, causing Kaidan to instantly stand at attention next to Anderson.

"Anderson, there's an incoming message from Admiral Hackett. He says it's urgent that you hear what he has to tell you."

"Thank you Udina, patch it through." Anderson turned to face the panel where Hackett's holo-image appeared before him. "Admiral Hackett, I hear you have something urgent to tell me." Udina began to walk out of office before Admiral Hackett even began speaking.

"Yes Councilor Anderson, Commander Alenko. Surveillance around Omega have reported that a Cerberus vessel just passed through the Omega 4 Relay." Once Admiral Hackett informed them of this new development, Kaidan knew there was only one possible ship attempting this impossible mission. "Reports show that it was the Normandy, registered under Commander Diana Shepard."

At that moment, Kaidan's omni-tool beeped once more, indicating that he had another incoming message. Opening up the message, he suddenly felt the world collapsing on him. It was another message from Diana, one with professionalism written all over it, and the one piece of information he needed to know. The reason she was working for Cerberus. He instantly felt sick for everything that he said to her on Horizon and for not going with her on this mission.

_**Alenko, **_

_**I'm sure that the Alliance had surveillance watching this ship, so you most likely already know we have just gone through the Omega 4 Relay by the time this message gets to you. I had Tali hack the ship and send this message to you before the AI on board could intercept it on our way through the Relay. This was the best way to ensure EDI, our AI, could not forward a copy of this to the Illusive Man. **_

_**Attached to this message is all the information that I could gather on the Collectors, the Reapers, and on Cerberus. Present this information to the Anderson, and hopefully he could use this and convince the Alliance and the Council that I was not crazy when I talked to them before. **_

_**Also, there are some things I wasn't able to tell you back on Horizon or in my earlier message. I DID DIE**____** when the Normandy went down two years ago. I remember it like it just happened. I got Joker to the escape pod, but I got separated from him when the Collectors launched another attack. My suit was damaged, the air hose was cut and I couldn't breathe out in space. And the reentry into the planet's atmosphere with a broken suit practically guarantees that I would not survive. From what Liara told me back on Illium, she was the one who gave my body to Cerberus. It was that or the Shadow Broker would give my body to the Collectors, the lesser of two evils I suppose. **_

_**Under the codename "Project Lazarus", Cerberus spent the last two years repairing my shattered body and brought me back to life. I don't know how, but I know the reason why I was brought back to life. They wanted to stop the Reapers. And that's where I come in. They feel I'm the only hope against the enemy. I'm not trying to justify their reasons. I'm just letting you know that I had no choice in this matter. There's one other reason I'm working with Cerberus besides the fact the Reapers need to be stopped. **_

_**Kaidan, I don't know how to tell you this. Or how you will react. The main reason I'm working for Cerberus is because they are holding someone important to me hostage. I can't let any harm come to her...I couldn't live myself if they did something. Her name is Abigail Dawn Shepard. She's...she's my daughter...**__**OUR**__** daughter! Cerberus gave her my surname because they didn't know that you were the father. **_

_**I was pregnant when I died. I was still in the early stages, about 2 months along. I was planning on telling you after that shakedown run near Alchera, but we were attacked by the Collectors. I don't know how they did it, but when they brought me back to life, they also brought her to life. They allowed her to develop normally in my womb until she was full-term, in which they delivered her through C-section. I was in a comatose state at the time, and was only informed about her existence after I told the Illusive Man that I refuse to work for Cerberus. He threatened me with her life.  
**_

_**If possible, please find her Kaidan. She needs to grow up with at least one of her parents around. I cannot risk her getting hurt, which is why I have to work with Cerberus. I'm hoping you can find her before my mission against the Collectors is over. If I survive, I want to be able to see her without worry that Cerberus would hurt our daughter. I want to know if she has your eyes or mine, I want to know all of that. **_

_**I'm sure Liara can provide you with information about Abigail. She works as an informer now. If you do not want this responsibility, I understand. I didn't tell you I was pregnant when I should have, and I'm sorry for that. But I love both of you dearly, and I will stop the attacks on our colonies. If not for the sake of humanity, or the rest of the galaxy, then for the man I love and our beautiful daughter. I hope to see you on the other side again.**_

_**- Shepard**_

Kaidan made his decision even before he finished the message from Diana. He looked up at Admiral Hackett, then at Anderson.

"I just received a message from Commander Shepard. It holds all of the information we need to convince the Council that there is a threat to the galaxy." Kaidan typed a few commands into his omni-tool so that he could forward the information to the Admiral and Councilor. He didn't want them to know the details regarding his relationship with Diana and their child, so he carefully removed it from the message before sending it.

"This is quite compelling evidence Commander. It's good to see that Shepard is still loyal to the Alliance. If you would excuse me gentlemen, but I need to begin sorting through this evidence immediately." Admiral Hackett gave them a salute before his image disappeared.

Anderson turned towards Kaidan. "I'm glad she was able to still trust us and send this information, though it seems like she doesn't expect to live through it." Kaidan nodded his head.

"It was a precautionary measurement that she took into account. Knowing Shepard, she wouldn't be able to die peacefully if she didn't have some way to ensure we could fight the Reapers with everything we got." Kaidan let out a sigh. He knew that in order to find his daughter, he might have to tell Anderson the truth about his relationship with Shepard. "There's something else that you should know Anderson. The reason for Shepard's alliance with Cerberus."

"Oh? Did she tell you in the letter?" Anderson was surprised that Kaidan had mentioned it. He didn't see it in the letter, but he figured there were some things in there that were for the eyes of her former Lieutenant alone.

"Sorry Councilor. I didn't want her image to be tarnished so I omitted some information when I forwarded it to you and Admiral Hackett. But yes, she did tell me in the letter." Kaidan looked a little bit sheepish for admitting he omitted information from the message voluntarily.

"What is it then?" Anderson was getting slightly curious about the whole letter now.

"They have a hostage that they're using against her. Someone very personal to her." Anderson gave Kaidan a suspicious look.

"How close are we talking here Alenko?" Kaidan hesitated before continuing on.

"Um...I don't know if Shepard would want people knowing about this Sir..." Anderson started to get the feeling that this person is someone very close to Shepard.

"Then this is completely off the record. You know that I fully support Commander Shepard against the Reapers. And if Cerberus is forcing her to work for them, then I'd like to know why." Anderson figured this would be the only way for Alenko to be completely honest to him about the letter.

"Well, then all right. The person that Cerberus is holding hostage is a young child named Abigail...Shepard's daughter..." Kaidan trailed off to let the information sink in.

"What? Shepard's daughter?!" Anderson couldn't believe what he was hearing. He knew that things between Alenko and Shepard were borderline flirting and fraternization. But he never thought they actually crossed that line.

"Yes Sir. Apparently, she was approximately 2 months pregnant when the Normandy was attacked. When Cerberus brought her back to life, they indirectly did the same thing to the child. They are using her daughter as leverage to keep Shepard in check." Kaidan let out a frustrated sigh. "I know Cerberus plays dirty, but even this is pretty low of them to use a child as a hostage." Anderson gave Kaidan a knowing look.

"And I assume you know the father of Shepard's child?" Kaidan's eyes grew wide with surprise, and hesitantly looked at Anderson.

"Uh well...is this still off the record?" Anderson noted that the COmmander was starting to look fairly uncomfortable with where the conversation was heading.

"Like I said Alenko, this is all off the record." Anderson gave him an encouraging smile, hoping that he would continue with the details.

"If that's the case. Then um...Sir, I am the father." Anderson just nodded his head to Kaidan.

"Hm. I figured that there was something personal between you and Shepard." Anderson just shook his head. "On a personal level, I feel that the two of you are prefect for each other. On a professional level, I don't know how I'm going to handle this just yet." Kaidan nodded his head in understanding. He knew that if Anderson found out, he would have to do take some disciplinary action since it occurred while she was his Commanding Officer. "Do you have an idea where Cerberus is holding her right now?" Kaidan shook his head, a frown beginning to form on his face.

"No, Shepard wasn't able to find out that information. Said it was too risky for her to look for Abigail while under the watchful eye of Cerberus. She suggested that I start with Illium and talk to an old friend there, Liara T'soni." Anderson was a bit surprised with this piece of information.

"Well, that is an interesting place to start. Why Dr. T'soni though?" He couldn't understand why Shepard would suggest Alenko to start with the Prothean archeologist.

"Shepard ran into Liara while she was at Illium. From what she told me in the message, Dr. T'soni is no longer an archeologist, but an informer now." Understanding dawned on Anderson's face.

"Meaning, she works for the Shadow Broker." Kaidan nodded his head.

"If anyone would know where my daughter is, she would. Shepard asked me to try and find her, so I will do everything I can to fulfill her wish." Kaidan turned around and started towards the door, but Anderson had to tell him one more thing.

"Alenko, be careful now. Cerberus will probably have surveillance on the child, so it won't be easy. Use your Spectre status wisely. The Terminus System is not very fond of them entering their area."

"I know Sir. Thank you for understanding." As Kaidan walked out the door towards his ship, he swore he could hear Anderson say something, but the closing doors made it impossible for him to be sure he heard the man correctly.

"Good luck, Kaidan. I hope you find your daughter."

* * *

**Author's Note:**

**Dun Dun Dun! I'm debating whether if or not I want to continue elaborating this story. I know people have had similar ideas, and I won't lie about that. Part of the idea that Shepard was pregnant during the beginning of ME2 has been tossed around a lot here. I just wonder what would Kaidan do if it turns out the child was brought back as an indirect result of Project Lazarus, and Shepard wanted him to know and all of that. **

**Yes, if you caught that subtle detail I added, this isn't true in the game. But his files are pretty classified so I wonder what that means. See if you can spot what I'm talking about! ^_^  
**

**Reviews are welcome and much appreciated! I would like to improve where needed so you don't have to read a bunch of plop.  
**


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